I think they use two pureftpds (as i wrote above, you can´t bind one pure--ftpd instance to two ports) with different configs and different startup-scripts.
To do this, you have to copy and adjust the init-script /etc/init.d/pure-ftpd-mysql and the wrapper-script /usr/sbin/pure-ftpd-wrapper. As long as you use the same sql-configs this should work with ispconfig.
You can install a 2nd ftp-server. But ispconfig does not supper vsftpd so you must create / update users by yourself.